\version "2.16.0"
\score
{
  \new PianoStaff
  <<
    \new Staff = "up" {
      <<
        \new Voice {
          \voiceOne
          \autochange
          \relative c'' {
            r2 r4 e4     % problem case: both voices go to base clef
            % r2. e4     % workaround
          }
        }

        \new Voice {
          \voiceTwo
          \autochange
          \relative c {
            r2 r4 a4     % problem case: both voices go to base clef
            % r2. a4     % workaround
          }
        }
      >>
    }

    \new Staff = "down" {
      \clef bass
    }
  >>
}